Contacts of the helix formed by residues 58 - 71 (chain D) in PDB entry 3DVA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 58 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER* 3.5 19.1 - - - +
178A GLN* 3.8 8.1 - - - +
183C GLU* 3.2 25.8 - - - +
187C PHE* 3.6 15.5 - - + -
28D GLU* 3.4 4.4 + - - -
56D PRO 2.9 8.1 + - - -
57D LEU* 1.3 76.1 - - - +
59D GLU* 1.3 61.5 + - - +
60D SER 3.3 0.2 - - - -
61D GLY 3.2 0.3 + - - -
62D ILE* 3.0 32.8 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLN* 2.9 25.8 + - - +
28D GLU* 2.8 31.1 - - - +
57D LEU* 4.3 2.1 - - - +
58D ALA* 1.3 71.9 - - - +
60D SER* 1.3 62.7 + - - +
62D ILE* 3.3 12.9 + - + +
63D GLY 3.0 18.4 + - - -
80D ILE* 4.3 16.1 - - + +
81D GLN 5.6 1.1 + - - +
85D PHE* 3.9 36.2 - - + +
88D GLU* 3.8 21.2 - - + +
89D VAL* 3.3 21.0 - - + +
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLN* 5.4 0.4 + - - -
149C ILE* 3.1 17.2 - - - +
180C ASP* 2.5 29.5 + - - -
183C GLU* 3.3 18.1 + - - -
58D ALA 3.3 0.4 - - - -
59D GLU* 1.3 77.7 - - - +
61D GLY* 1.3 59.0 + - - +
63D GLY 3.3 1.0 + - - -
64D GLY 3.0 22.3 + - - -
88D GLU* 3.3 25.5 + - - +
89D VAL* 4.0 7.0 - - - -
91D ASP* 6.1 1.2 - - - +
92D SER* 3.6 4.9 + - - -
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ILE* 4.1 16.8 - - - +
183C GLU* 2.7 20.7 + - - -
187C PHE* 3.6 24.9 - - - -
58D ALA 3.2 4.5 + - - -
60D SER* 1.3 71.6 - - - +
62D ILE* 1.3 60.5 + - - +
64D GLY 3.3 0.7 + - - -
65D LEU* 2.8 31.5 + - - +
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Residues in contact with ILE 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C PHE* 4.2 5.2 - - + -
26D PHE* 3.6 13.9 - - + +
27D GLY* 4.1 11.4 - - - -
28D GLU* 4.1 23.6 - - + +
55D THR* 3.4 31.9 - - - +
56D PRO 4.4 0.4 - - - +
58D ALA 3.0 20.8 + - - +
59D GLU* 3.3 13.9 + - + +
61D GLY* 1.3 76.0 - - - +
63D GLY* 1.3 61.5 + - - +
65D LEU* 3.5 5.7 + - - +
66D ALA* 3.1 22.5 + - - +
78D PRO* 3.9 23.3 - - + -
79D GLU 4.4 13.9 - - - +
80D ILE* 6.0 4.3 - - + -
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU 3.0 14.3 + - - -
60D SER 3.3 3.6 + - - -
61D GLY 3.2 0.2 - - - -
62D ILE* 1.3 76.0 - - - +
64D GLY* 1.3 62.8 + - - +
66D ALA* 3.3 8.0 + - - +
67D ILE* 3.1 26.9 + - - +
78D PRO* 6.0 1.3 - - - -
89D VAL* 3.9 5.8 - - - -
92D SER* 3.7 20.0 - - - -
97D MET* 4.1 7.0 - - - +
114D ILE* 6.4 0.4 - - - -
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Residues in contact with GLY 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ILE* 3.2 39.1 - - - +
150C GLN* 3.5 7.2 - - - -
60D SER 3.0 10.7 + - - -
61D GLY 3.8 1.8 - - - -
63D GLY* 1.3 72.8 - - - +
65D LEU* 1.3 59.9 + - - +
67D ILE* 3.3 8.0 + - - +
68D GLY* 2.9 26.2 + - - -
92D SER* 3.6 3.2 + - - -
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ILE 3.6 1.7 + - - -
152C ALA* 4.0 9.9 - - + +
153C GLY* 3.6 26.6 - - - +
156C LEU* 3.8 28.9 - - + -
187C PHE* 4.4 14.1 - - + -
191C PHE* 4.1 22.9 - - + -
26D PHE* 4.0 23.1 - - + -
53D PHE* 4.1 7.4 - - + -
55D THR* 4.2 6.5 - - + -
61D GLY 2.8 17.7 + - - +
62D ILE* 3.6 5.8 - - - +
64D GLY* 1.3 78.0 - - - +
66D ALA* 1.3 56.5 + - - +
68D GLY 3.4 0.2 + - - -
69D LEU* 2.9 38.8 + - + +
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Residues in contact with ALA 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.7 22.1 - - + -
62D ILE 3.1 13.3 + - - +
63D GLY* 3.5 10.3 - - - +
65D LEU* 1.3 74.2 - - - +
67D ILE* 1.3 60.1 + - - +
69D LEU* 4.5 0.2 - - - -
70D ALA* 3.0 24.4 + - - +
76D PRO* 3.2 23.4 - - + +
78D PRO* 3.9 14.6 - - + -
97D MET* 4.7 1.8 - - + -
112D ILE* 3.7 12.2 - - + +
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Residues in contact with ILE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C LEU* 6.0 0.2 - - + -
150C GLN* 3.9 31.6 - - + +
63D GLY 3.1 17.5 + - - +
64D GLY* 3.3 5.6 + - - +
66D ALA* 1.3 72.3 - - - +
68D GLY* 1.3 66.4 + - - +
70D ALA* 3.2 4.9 + - - +
71D LEU* 3.1 26.5 + - + +
92D SER* 3.5 32.8 - - - +
96D GLN* 3.6 18.6 - - + -
97D MET* 3.9 20.2 - - + +
100D ILE* 4.7 7.2 - - + -
110D MET* 3.5 25.5 - - + +
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLN* 3.4 13.0 + - - +
153C GLY 3.5 8.1 - - - -
154C VAL* 3.4 35.2 - - - -
64D GLY 2.9 12.2 + - - -
67D ILE* 1.3 76.7 - - - +
69D LEU* 1.3 59.8 + - - +
71D LEU* 3.2 16.3 + - - +
72D GLN* 3.4 7.6 + - - +
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLY 3.4 17.0 + - - +
156C LEU* 3.9 21.1 - - + -
157C GLY* 3.6 20.4 - - - +
160C MET* 4.2 10.8 - - - -
24D LEU* 4.0 11.4 - - + -
26D PHE* 3.7 32.5 - - + -
53D PHE* 4.6 1.3 - - + -
65D LEU* 2.9 35.3 + - + +
66D ALA 3.8 3.8 - - - +
68D GLY* 1.3 71.9 - - - +
70D ALA* 1.3 61.9 + - - +
72D GLN* 2.9 20.3 + - - +
74D PHE* 3.2 29.8 + - + +
76D PRO* 4.2 6.7 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D ALA 3.0 18.3 + - - +
67D ILE 3.5 5.4 - - - +
69D LEU* 1.3 75.3 - - - +
71D LEU* 1.3 61.6 + - - +
72D GLN 3.1 0.2 - - - -
73D GLY* 3.2 13.7 + - - -
74D PHE 3.6 12.5 - - - +
76D PRO* 3.9 8.0 - - + +
109D HIS* 4.1 9.1 + - - +
110D MET* 3.5 21.5 - - + -
111D PRO* 4.0 21.8 - - + +
112D ILE* 4.2 2.9 - - + -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PHE* 4.1 12.9 - - + -
99C LEU* 4.9 1.3 - - + -
138C LEU* 3.6 39.0 - - + -
150C GLN* 5.1 0.9 - - + +
154C VAL* 3.7 24.0 - - + -
67D ILE* 3.1 23.8 + - + +
68D GLY* 3.4 9.4 - - - +
69D LEU 3.2 0.2 - - - -
70D ALA* 1.3 76.2 - - - +
72D GLN* 1.3 65.4 + - - +
73D GLY 3.4 1.6 + - - -
100D ILE* 4.9 0.7 - - + -
108D TYR* 3.6 44.4 - - + -
109D HIS 5.1 1.3 - - - +
110D MET* 3.6 20.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il